Do you know about phosphodiester linkages? Each nucleotide is bound to the other (in the same chain) by these, and they are between the phosphate groups and terminal hydroxyl groups. The end starting with the phosphate is the 5' end and the terminal hydroxyl end is the 3' end. DNA runs antiparallel. When DNA is being constructed nucleotides are most easily added to the 3' end, so that is the direction of chain elongation. Think of it like a stream, which is also why the terms upstream and downstream are used. 5' is the waterfall. Each strand has its end, but they are opposite of each other. Does that help?

Sorry for jumping in the discussion. The explanation of plasmodesmata11 is complete for me to understand Yuuki's question. But it raises an other related question: so the DNA molecule has two strands twisting together and orienting in opposite directions (3' -> 5' and 5' -> 3'). It looks to me that the double DNA is symmetric in two directions, so why it again twists itself in only one direction of the clock, but not the other way around? And apart from the twisting structure, is there any other asymmetry biological effect the double strand DNA molecule, say for example: replication in one direction (of the double strand, say from the long arm of chromosomes to the short arm of chromosomes, I do not mean the difference between lagging and leading strand...) is better than the other?Hope I did not drive the topic so far away...Thanks.

Yeah, to add to what Jack said there are several forms of DNA, usually depending on how hydrated they are or what nitrogenous bases they contain. There can be left or right hand helices, the measurements between the bases can be wide or short, etc. There are forms B (biological), A (dehydrated), C (more dehydrated), D and E (no guanine), P (interior phosphates), and Z, which has only C-G bonds